Some suggested on Monday that the council was prioritising tourism over agriculture, which the council denied.

Experts called to give evidence on biodiversity loss on Wednesday said it had happened at a large scale and would continue to happen unless intensive farming was curtailed.

Nicholas Head, a plant ecology advisor at the Department of Conservation (DOC), said the area's rare ecosystems were "very poorly protected" and were being increasingly lost to development.

There were at least 83 species recorded as threatened or at risk on the basin floor alone, he said.

"Intensive agricultural practices using cultivation and irrigation have caused widespread and permanent loss of natural ecosystems and indigenous biodiversity across the Mackenzie Basin," he wrote in his written evidence.

"From my observation, the majority of the losses have resulted from changes in farming methods … My understanding is that change has occurred with little scrutiny of the significant ecological values that may have been affected, despite them being areas that were considered to have supported significant ecological values."

Under cross-examination, Head said the loss of rare ecosystems meant protecting those still there was increasingly urgent.

"Because the Mackenzie has such a distinct ecological character, the more you lose of these ecosystems, the less chance you have to protect representative examples of those ecosystems elsewhere.

"It underpins why some of these remaining ecosystems are nationally significant."

DOC senior ranger of biodiversity Dean Nelson said if development continued at its current rate it risked creating isolated populations of some species.

"For a lot of species it becomes difficult for them to maintain their populations if they're restricted to little pockets and don't have the ability to traverse large areas," he said.

"Invertebrates, particularly lizards … they're not going to cross areas of green grass. If they've got existing vegetation and habitats then they can continue to move."

In his written evidence he said that nutrient run-off could have an impact on fresh water species.

When asked if Environment Canterbury's nutrient rules for the area would mitigate that, he said he was not convinced.

"I don't think we've seen that it has necessarily worked."

Other experts, including agronomist Warwick Scott and ecologist Susan Walker, expressed concern about the rate of development in parts of the basin.